9T62 | pdb_00009t62

Crystal structure of ortho-aminophenol oxidase SmNspF from Streptomyces murayamaensis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-D6RTB9-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293.15	Mixing 5 microliter of SmNspF solution (10 mg/ml) with 4 microliter of reservoir solution (8% PEG 8000, and 800.0 mM Lithiumsulfate , 20.0 mM TRIS, 16.1 mM HCl)

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.189	α = 90
b = 86.189	β = 90
c = 88.245	γ = 120

Symmetry
Space Group	P 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 4M	Vertical CRL / Horizontal Eliptical mirror	2022-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	12.812 keV	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.95	74.64	99.1	0.919	2.4	3.7		52735			46.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2			0.059

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.4	74.64	28394	1416	98.958	0.186	0.1827	0.1539	0.2376	0.1989	RANDOM	60.948

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
17.579			17.579		-35.157

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	15.531
r_dihedral_angle_3_deg	14.898
r_dihedral_angle_6_deg	13.122
r_mcangle_it	10.757
r_scangle_it	10.216
r_dihedral_angle_1_deg	7.744
r_mcbond_it	7.695
r_scbond_it	7.497
r_dihedral_angle_2_deg	6.334
r_angle_refined_deg	1.969
r_nbtor_refined	0.291
r_nbd_refined	0.195
r_symmetry_nbd_refined	0.181
r_ncsr_local_group_1	0.141
r_xyhbond_nbd_refined	0.132
r_symmetry_xyhbond_nbd_refined	0.128
r_chiral_restr	0.096
r_gen_planes_refined	0.011
r_bond_refined_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4977
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
gemmi	data extraction
autoPROC	data reduction
MOLREP	phasing